Thursday, December 20, 2012

Over the years the number of plants being traded worldwide increased and with that the
chance of harmful organisms spreading was greatly enhanced. At the same time,
the taxonomic knowledge available to identify harmful quarantine
organisms via their visual characteristics decreased gradually.

The resulting
economic damage is significant and shows how vital the development of accurate identification tools
for plant pathogens and pests is.

Three years ago researchers from 15 mainly European nations founded QBOL a project financed by the 7th Framework
Program of the European Union with the aim to make collections harboring
plantpathogenic quarantine organisms publicly available.One main goal was to sequence genes from selected species on the EU and EPPO relevant lists . Over the 3 years the sequences, together with taxonomic features, were
included in an internet-based database system called Q-Bank.

Some 18 000 sequences are available on the database and serve as identification and detection reference for
phytosanitary organizations such as national plant protection organizations,
general inspection bodies, and private laboratories. The project officially ended in September 2012 but the database will be continuously maintained and curated. However, as usual funding is not unlimited and similar to all other databases out there Q-Bank is looking for more suistainable solutions.

Tuesday, December 18, 2012

Phytoplasmas are bacterial plant pathogens that cause significant losses in
agricultural production worldwide. They are causing a wide variety of symptoms that can range from mild yellowing to the death of infected plants. They are most prevalent in the tropical and sub-tropical
regions of the world. Phytoplasmas are transmitted by
hemipteran insect vectors such as leaf hoppers, in which the bacteria are also able to survive and replicate.

Phytoplasmas infect over 200 plant species, prominent examples are coconut, sugarcane, and sandalwood. They are are considered of quarantine relevance e.g. in the EU, which means that their spread is especially tightly regulated. There are no fully resistant crop varieties currently available. Therefore, main
disease management strategies are limited to control of the vectors provided that those are known, and the elimination of infected plants. There is a great need for reliable and efficient methods for identification for this group of pathogens, and our standard barcoding regions are likely inefficient.

Witches' broom caused by Phytoplasmas

A group of European researchers tested a set of primers amplifying a fragment of the so-called tuf gene (Elongation factor Tu) for their potential to serve as a DNA barcode for phytoplasmas. Elongation factor Tu is a key protein involved in the process
of protein biosynthesis. Standard in DNA-based bacterial identification is 16S rRNA. Analysis and alignments showed that important
groups of phytoplasmas could readily be identified. While being shorter, the tuf barcode provided clear resolution at both group and subgroup levels compared to the 16S rRNA gene making it an ideal candidate.

This work was part of the QBOL initiative, which aims to develop a DNA barcode-based
identification system for pests and pathogens with
a focus on quarantine organisms. The project has started to release data in a specific database - q-bank.

Monday, December 17, 2012

My apologies for not posting as often as usual but first I caught a pretty nasty bug and stayed in bed for two days and this week we are working on the finishing touches of the new iBOL Barcode Bulletin that should come out at end of this week. That work keeps me quite busy. Nevertheless, here a little story about a little newly discovered skipper butterfly that was found on Jamaica.

Troyus turneri

Researchers from the Florida Museum of Natural History used morphology, especially comparisons of the
insect's genitalia, and DNA Barcoding to determine that it was not only a new species but represented a new
genus. Troyus turneri is a small butterfly with a wingspan of little more than 1 cm but according to some of the authors has the potential to be a flagship species for Jamaican
habitat conservation, because it's a black butterfly with gold stripes living in a
green habitat, which together comprise the Jamaican national colors. The resaerches hope the native butterfly will encourage conservation of the
country's last wilderness where it was discovered: the Cockpit Country. It is the first butterfly discovered in Jamaica since 1995. The island was thought to be well-known, but now 17 years later the new encounter really shows the need for biodiversity studies in the region.

The genus was named Troyus for the town of Troy, which is nearest to the
region of the Cockpit Country where it was collected, and the species
was named for Thomas Turner, an expert on Jamaica butterflies who
contributed to its discovery.

In case of further species discoveries in this genus may I humbly suggest names such as Troyus marleyi or Troyus toshii :-)

Head cream-white; second segment of labial palpus cream-white, brown at base and apex, and tinged brown medially; thorax and tegula mottled cream and light brown, or rarely plain cream. Forewing length ♂, 9.2–11.4 mm, ♀, 9.1–10.0 mm; forewing ground colour predominantly cream, with some greyish mottling, particularly extensive in material from the Pyrenees; oblique fascia of raised black scales from basal part of costa to dorsum; three black dots of raised scales edged with ochreous in middle of forewing; two further spots before whitish subapical fascia; apical part greyish with black spots along termen; fringes grey. Hind wing grey-brown to moderately light grey, with some variation depending on substrate.

For those (like me) who find that too complicated and hard to understand I have pasted some images of males of the moth as shown in the paper.

I think this is a very nice gesture to honor Paul and the fact that without his vision, energy, and endurance DNA Barcoding would have never been such a success story. And what would be a better fit than naming a representative of the group he is most passionate about after him?

(2) Earlier this year our lab helped with an investigation aimed to
provide species identification on subsamples taken from a hammer for the OntarioSociety for the Prevention of Cruelty to Animals (OSPCA) and Toronto Police
Service. Somebody was suspected to have killed a dog with a hammer. Hair and blood samples could perhaps confirm that the hammer owned by the suspect was the weapon.

Close-up showing a hair that was used to retrieve DNA

The lab was able to retrieve several short length sequences still long enough to be reliably matched to reference sequences of the domestic dog, Canis lupus familiaris. They were also able to retrieve some human DNA from the handle (not surprisingly) which could have been used for a STR profile.

However, that wasn't even necessary as the suspect confessed when confronted with the initial evidence provided by DNA Barcoding.

Researchers from Italy were able to do direct imaging of double stranded λ-DNA in
the A conformation, obtained by combining a novel sample preparation
method based on a super hydrophobic DNA molecule self-aggregation process
with transmission electron microscopy (TEM). A-conformation DNA is thought to be one of three biologically active double helical structures along with the conformations B and Z. It is a right-handed double helix fairly similar to the more common and well-known B form, but with a shorter more compact helical structure.

A-DNAs superstructures used for image simulations

This is the first time that humans have captured direct photos of DNA. At present, the method only works with superstructures of DNA made up of six
molecules wrapped around an seventh acting as a core. That's because the
electron energies are high enough to break up a single DNA molecule. However, according to the researchers the problem could likely be solved by using a lower-power electron scope. With this technique, researchers should be able to see how single molecules of DNA interact with other biomolecules.

Thursday, December 6, 2012

I have to admit it is going to be a fishy week on this blog but what can I do. After all one chooses what's close to ones heart ;-)

When it comes to DNA Barcoding in the media the really big stories had to do with fish or more precisely the seafood market. That started with the famous 'Sushigate' where two high school students used the method to show that many items on menus in seafood restaurants were simply mislabeled.

Frozen Tilapia - unfortunately often sold as red snapper

Quite a few broadcasters and newspapers took the idea and conducted their own investigations. Among those the Boston Globe. A year ago they tested seafood from Boston and with our help they found out that about half the time fish bought at restaurants across the region was mislabeled. They concluded:

Massachusetts consumers routinely, and unwittingly, overpay for less
desirable, sometimes undesirable, species - or buy seafood that is
simply not what it is advertised to be. In many cases, the fish was
caught thousands of miles away and frozen, not reeled in by local
fishermen, as the menu claimed. It may be perfectly palatable - just not
what the customer ordered. But sometimes mislabeled seafood can cause
allergic reactions, violate dietary restrictions, or contain chemicals
banned in the United States.

Over the past several months, the
Globe collected 76 seafood samples from 58 of the restaurants and
markets that sold mislabeled fish last year. DNA testing on those
samples found 76 percent of them weren’t what was advertised.
Some restaurant operators who repeatedly mislabeled fish blamed
suppliers. Others said naming inconsistencies were the result of
clerical errors. Several made only partial revisions to their menus.

The main problem is that legislation hasn't caught up on the problem. Restaurants and suppliers know they will not face punishment for mislabeling fish. The Food and Drug Administration, which maintains a list of acceptable
market names for fish species, has historically focused efforts on food
safety, rather than economic fraud such as seafood substitution. However, they have already implemented DNA Barcoding as tool for seafood identification. Only regulation of the nation's seafood trade has to catch up which of course is a long and bureaucratic process.

I had been in touch with the Vancouver Animal Defense League for a while already as a result of a blog post back in August in which I reported about efforts to ban shark fins from Canadian cites and provinces. What was lacking in all discussions and news releases was a clearer picture of what species are actually sold in Canadian shops. Earlier investigations in US restaurants had given us an idea but the actual extend was unknown. When I received the fins I was pretty sure that some of them were from endangered or at least threatened species according to the IUCN Red List but I was very surprised to find out that 76% of all samples sequenced fell into those categories. This was far worse than I thought and demonstrates how dramatic the situation is.

If you want to get an impression of the dimension of the problem just go in one of the shops that sell fins as food or health products (if you happen to live close by). Have a look at the shelf's that are jam packed with dried fins and imagine that 3/4 of them are likely from species that are at least threatened. Now think of how many such shops there are.

Yesterday our results officially went public. I know that advocates of a province-wide ban of shark fin products in British Columbia are very positive as our findings will help them to substantiate their claims .

Today Google launched their Global Impact Awards
to support organizations using technology and innovative approaches to
tackle some of the toughest human challenges. From real-time sensors
that monitor clean water to DNA barcoding that stops wildlife
trafficking, the first round of awards provides $23 million to seven
organizations changing the world.

Among them is the Consortium for the Barcode of Life (CBOL) at the Smithsonian Institution that will use
its $3 million Impact Awards grant to create and begin implementing DNA Barcoding
as an actionable tool for protecting the world’s most endangered wildlife. Working
with researchers in six developing countries, CBOL will build a public library of
DNA barcodes that law enforcement officials can use to identify confiscated
material. The library is supposed to comprise approximately 2,000 endangered
species and 8,000 species that are closely related to them or are
commonly confused with them. The reference library will be part of GenBank.

Well, first of all, congratulations to CBOL for acquiring this grant. This is a great accomplishment especially in times where funding for biodiversity science is not on top of the list. The greater the news that the money is dedicated to advance the protection of endangered species.

Of course short press releases leave the interested reader with a lot of open questions and I have quite a few but I am sure there will be enough time for a closer look as soon as the project is up and running.

Monday, December 3, 2012

Daphnia are one of the several small aquatic crustaceans commonly called water fleas because of their erratic swimming style. They live in various aquatic environments ranging from acidic swamps to freshwater lakes.

The identification of Daphnia species is difficult particularly in the so-called Daphnia pulex species complex . Determination of species based on morphological methods is only possible in a small number of species. Most others lack reliable morphological traits as a result of morphological stasis combined with a poor taxonomy. Initially the Daphnia pulex complex was considered to comprise of a few species but in recent years a number of new species have been identified genetically. Furthermore, each
of these taxa comprises separate species in North America and
Europe, despite carrying the same names.

There seems to be no alternative to a DNA Barcoding approach although there is an additional complicating factor, because similar to several other Daphnia species, North American Daphnia pulex members are able to form viable hybrid populations with Daphnia pulicaria. Any analytics should therefore include an allozyme analysis to confidently determine species status

New Zealand has only one recognized native Daphnia species, the relatively uncommon Daphnia carinata. These first confirmed recordings of members of the Daphnia pulex complex in New Zealand come from South
Island lakes that are popular for overseas recreational fishers, indicating a possible means of introduction in association with fishing and boating equipment.

The question is if this recent invasion will have any perhaps detrimental effect on the local fauna and flora. The authors think that the establishment of non-indigenous Daphnia might have large effects on lake and pond biota by probably reducing the abundances of both phytoplankton and other zooplankton (particularly rotifers).